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To our knowledge, the cancer pharmacogenetics article by Marsh et al in this issue of the Journal of Clinical Oncology is the largest published pharmacogenetic study of carboplatin and taxanes, focusing on the potential association of candidate polymorphisms with treatment toxicity and disease response outcomes. It is a model for how collection of whole blood samples for DNA in a phase III clinical trial (which, by design, prospectively collects important phenotype data with unbiased treatment assignments) enables high quality pharmacogenetic research. Strikingly, but appropriately, it is published with no positive findings to report. Attaining the proposed benefits of the Human Genome Project requires an iterative process of hypothesis generation and hypothesis testing. It is not disconcerting that this study failed to confirm previously published associations between various polymorphisms and outcomes from combined carboplatin and docetaxel or paclitaxel regimens. It is a signal that more work might be done, and should be a warning to those investigators who have jumped from small, hypothesis-generating pharmacogenetic studies with borderline P values into large prospective randomized trials to test the utility of the putative pharmacogenetic test, but without first attempting to validate the association. The first two pharmacogenetic tests in oncology, for thiopurine methyltransferase (TPMT) and UGT1A1 deficiencies, were developed through a candidate gene/polymorphism approach. In each case, clinical observations led to multiple preclinical studies, including testing of the relationship between specific functional polymorphisms of TPMT and UGT1A1 and enzyme function. Ultimately, small prospective clinical trials were conducted where the primary objective was to confirm the relationship between the genetic variant and excess exposure and consequent toxicities from 6-mercaptopurine and irinotecan, respectively. Use of this approach does not ensure successful development of a pharmacogenetic test. While dihydropyrimidine dehydrogenase deficiency is heritable and leads to excess exposure to fluorouracil and consequent toxicity, it has been associated with numerous polymorphisms in the DPYD gene, but with each single nucleotide polymorphism (SNP) found at different frequencies in different populations. Hence, any single genotype has insufficient negative predictive value to be clinically useful. At the same time, adhering to the principles of the candidate gene/polymorphism approach has instead led investigators to focus efforts on developing phenotype-based assays. Marsh et al utilized an approach likely to be of increasing importance in pharmacogenetics. They were able to test specific hypotheses regarding candidate polymorphisms in a large clinical trial data set because DNA had been collected and was available for analysis. By removing biases of treatment assignment, completing data collection within a specified timeframe, and by careful phenotyping for features of immediate clinical relevance, large clinical trials of cancer therapy provide important data sets for developing pharmacogenetic tests. Since preclinical testing does not assess the magnitude of effect for a candidate gene/polymorphism in the clinical setting, genotyping for associations with previously collected phenotypic data provides a crucial opportunity for validating the candidate polymorphism, without incurring the expense of a new prospective study. Investigators could change the development plan based on these tests and increase the likelihood of success in the prospective setting, for example by increasing the number of polymorphisms typed to capture better the relevant genetic variants affecting a treatment phenotype or by switching to a phenotype test altogether. The study by Marsh et al is also a lesson in how to assess appropriately the relationship between candidate polymorphisms and clinical outcomes. One critical obstacle to successful development of a genotype-based diagnostic test is the high number of spurious associations. Each patient has 10 base pairs (bp) in his/her genome. With SNPs occurring every 100 to 300 bp, taken to the extreme, each patient has 10 potential hypotheses to test for association with each clinically relevant phenotype of interest. With a P value cutoff of .05, 500,000 SNPs will demonstrate a significant association with one phenotype by chance alone. As increasing numbers of phenotypes or combinations of polymorphisms are considered, the multiple-hypothesis testing in the same data set increases the number of false-positive associations. With so many expected false-positive associations, a nominally significant P value merely suggests, but does not confirm, a hypothesis that would warrant additional testing. Marsh et al addressed this problem for their association of 27 candidate polymorphisms with six clinical phenotypes first by predetermining an acceptable falsediscovery rate and screening these SNPs in 609 randomly selected patients with univariate models. They then incorporated the two SNPs passing the false-discovery rate criteria into a multivariate model that was then tested in 305 patients, and the two SNPs proved to be JOURNAL OF CLINICAL ONCOLOGY E D I T O R I A L VOLUME 25 NUMBER 29 OCTOBER 1

2537^ Background: Test the predictive value of gene polymorphisms potentially linked to panitumumab and irinotecan pharmacodynamics. Methods: 45 patients with metastatic CRC refractory to standard therapy were enrolled in this ancillary pharmacogenetic study as part of a phase II trial that included 63 patients. Inclusion required wild-type KRAS tumor status (codons 12-13, analyses performed in each center). After inclusion, central KRAS re-assessment was performed (codons 12-13-59-61) and 9 patients over 45 were found to carry a KRAS mutation. Patients received panitumumab (6 mg/kg, day 1) associated with irinotecan (180 mg/m2, day 1), Q2W until disease progression or unacceptable toxicity. Analyzed polymorphisms on blood DNA were : EGFR (CA repeats in intron 1, -216G>T, -191C>A), EGF (61A>G), CCND1 (870A>G), UGT1A1 (*28). Results: Cutaneous toxicity imputable to panitumumab i.e. folliculitis and paronychia was not linked to EGFR, EGF or CCND1 polymorphisms. Diarrhea (12 grade 1, 13 grade 2, 8 grade 3) was linked to CCND1 polymorphism: 22% grade 2-3 in AA patients vs 63% in AG+GG patients (p = 0.007). As expected, neutropenia (6 grade 1, 4 grade 2, 5 grade 3) was more frequent in patients bearing the *28 allele of UGT1A1 gene (33% grade 2-3 vs 5% in *1/*1, p = 0.020). In these 45 patients, response rate, progression-free survival and overall survival (OS) were only significantly related to re-assessed KRAS status. Of note, a tendency for a longer OS was observed in patients bearing the *28 allele of UGT1A1 gene (p = 0.091, analysis adjusted for KRAS). Interestingly, the frequency of KRAS mutation was higher in patients with long CA repeats in EGFR gene intron 1: 54.5% i.e. 6 mutated patients among the 11 patients with both alleles ≥17 vs 10.5% i.e. 2 mutated patients among the 19 patients with intermediary alleles vs. 6.7% i.e. 1 mutated patient among the 15 patients with both alleles

e14009 Background: Several studies have been performed to evaluate the usefulness of neoadjuvant treatment based on oxaliplatin and 5-fluorouracil in locally advanced rectal cancer. However, preope...

e15087 Background: There have been reports about the ethnic difference of toxicity profile to sunitinib. In Asian population, thrombocytopenia, neutropenia, and hand-foot syndrome (HFS) were more frequently reported. We aim to assess the pharmacogenetic determinants of these toxicities, which were developed after treatment with sunitinib in Korean patients with metastatic renal cell carcinoma (mRCC). Methods: A pharmacogenetic study was performed in 51 patients with mRCC treated with sunitinib 50mg orally, once daily (4 weeks on-2 weeks off). This study included 41 male and 10 female. Clear cell type in 48 patients (94.1%) and papillary type in three patients (5.9%) were observed. Detailed toxicities of sunitinib, including thrombocytopenia, neutropenia, and HFS during treatment with sunitinib were prospectively collected. A total of 10 single nucleotide polymorphisms (SNPs) in 7 candidate genes (CYP1A1, ABCG2, ABCB1, PDGFRa, VEGFR2, RET, and FLT3) were genotyped and their relationship with toxicities wer...

3101 Background: We investigated candidate pharmacogenetic markers of chemotherapy toxicity in a prospective study of metastatic colorectal cancer (mCRC) patients. Methods: We recruited115 mCRC patients treated with irinotecan-based chemotherapy. The primary objective was to assess the relationship between genetic variations and toxicity. Toxicity was prospectively evaluated according to NCI-CTCAE v3.0 criteria. The secondary objective was to explore the relationship between genetic markers and tumor response. Twenty polymorphisms in the UGT1A metabolic gene and 19 in the ABC/OATP transporter genes were assessed. Results: In univariate analyses, several functional UGT1A variants, including UGT1A1*28 (c. -54--53 TA7), as well as ABCC1 and ABCB1 variants were shown to significantly influence severe hematological toxicity. In multivariate analyses, UGT1A6 c.184 and UGT1A7 c.208 were associated with severe neutropenia (odds ratio [OR] 3.01, 95% CI [1.42-6.36], p=0.004; OR=2.53, 95% CI [1.19-5.35], p=0.016, re...

4069 Background: Our purpose was to test the predictive value of germinal gene polymorphisms potentially linked to cetuximab, fluoropyrimidine and irinotecan pharmacodynamics on toxicity, clinical response, time to progression (TTP) and overall survival (OS). Methods: 52 patients with advanced CRC were enrolled in an ancillary pharmacogenetic study of the phase II CETUFTIRI trial (33 men, 19 women, mean age 63, range 36–84, PS 0–1). Treatment consisted in cetuximab (day 1-day 8-day 15, 250 mg/m2/week following a 400 mg/m2 loading dose) associated with irinotecan (day 1, 250 mg/m2) and UFT-folinic acid (day 1 to day 14, 250 mg/m2/day UFT, 90 mg/day folinic acid). Median number of administered cycles was 7 (range 1–8). The following gene polymorphisms were analyzed on blood genomic DNA: EGFR (CA repeats in intron 1, - 216G>T, -191C>A), EGF (61A>G), FCGR2A (131Arg>His), FCGR3A (158Phe>Val), UGT1A1 (TA repeats), TYMS (28 bp repeats including the G>C mutation on the 3R allele, 6 bp deletion in 3’ UTR), MTHFR (677C>T, 1298A>C). Results: Grade 3–4 toxicity was recorded in 59.6 % of patients. The toxicity score (sum of maximum grade for each toxicity pattern) was significantly linked to the FCGR2A genotype (median score 9, 9.5 and 13 in Arg/Arg, Arg/His and His/His patients, respectively, p = 0.035) and to the EGFR -191 genotype (median score 11 in CC patients versus 8.5 in CA patients, p = 0.040). Response rate was 49% (3 CR and 21 PR over 49 assessable patients) and was significantly higher in patients bearing the FCGR3A Val allele (62.1 % in Val/Val or Val/Phe versus 26.3 % in Phe/Phe, p = 0.020) or the TYMS 3RG allele (65.0 % versus 28.6 % in patients with no 3RG allele, p = 0.029). Gene polymorphisms did not influence TTP. A multivariate Cox analysis including gene polymorphisms and PS showed that overall survival was improved in patients bearing the FCGR3A Val allele (relative risk of death was 2.25 in Phe/Phe patients relative to Val-containing genotypes, 95% CI 1.03–4.91, p = 0.041). Conclusions: Present data suggest the importance of ADCC in cetuximab pharmacodynamics, as outlined by the role of FCGR gene polymorphisms on toxicity, responsiveness and survival. No significant financial relationships to disclose.

2505 Background: S-1 is an oral anticancer agent composed of tegafur (FT), CDHP, and oxonate. CYP2A6 is related to the biotransformation of FT to 5-FU. We evaluated associations of genetic variants of CYP2A6 with PK/PD of S-1 when combined with oxaliplatin in metastatic biliary cancer. Methods: This is a prospective study of patients with histologically confirmed metastatic adenocarcinoma of the biliary tract. S-1 was administered orally at a dose of 40 mg/m2 twice daily for 14 days followed by a 7-day rest period. For PK study, S-1 was given only once at day 1 of cycle 1. From day 2, it was administered twice daily. Oxaliplatin was administered intravenously at a dose of 130 mg/m2 for 2 hours every 3 weeks. CYP2A6 polymorphism (*1, *4, *7, *9 or *10) were genotyped. Results: A total of 49 patients were enrolled. Median age was 52 years (range 23–68) and male accounted for 63%. Thirty patients (61%) had intrahepatic cholangiocarcinoma and 10 (20%) gallbladder cancer. Response rate was observed in 24.5%. The median PFS and OS were 3.7 months and 8.7 months . Grade 3–4 adverse events include vomiting (22%), diarrhea (4%) and neutropenia (14%). The allele frequencies of CYP2A6*4, *7, *9 and *10 were 10.2%, 8.2%, 19.4%, and 4.1%, respectively. AUC0–24hr of 5-FU was 1030±617.3 hr*ng/mL (range 249.5–3969, CV: 59.9%). Log- transformed AUC0–24hr were significantly different for FT and 5-FU in the *1/*1 group; metabolic ratio (AUC0- 24hr of 5-FU/AUC0–24hr of FT) of the *1/*1 group was 1.85-times higher than the other group (90% CI 1.37–2.49). AUC0–24hr of CDHP was not significantly associated with CYP2A6 genotype. Despite differences in exposure, CYP2A6 genotypes were not significantly associated with diarrhea (P=0.0740), neutropenia (P=0.396) and clinical efficacy (response rate: P=0.583, PFS: P=0.916). Conclusions: CYP2A6 genotypes was associated with transformation of FT to 5-FU; however, this association did not translate into different clinical efficacy or toxicity. [Table: see text] No significant financial relationships to disclose.

3580 Background: Pharmacogenetic research holds the promise of individualizing cancer therapy by reducing inter-individual variability in drug response, thus enhancing efficacy and reducing toxicity. Past research has been limited due to the lack of a robust genotyping platform that can screen for single nucleotide polymorphisms (SNPs) in the dozens of genes known to be involved in drug disposition. We pilot tested the new Affymetrix Targeted Human Drug Metabolizing Enzymes and Transporter (DMET) 1.0 panel in an exploratory study of docetaxel and thalidomide. The DMET 1.0 panel tests for 1,229 genetic variations in 169 drug disposition genes, including 49 CYP450 genes, 73 non-CYP genes, and 47 transporters. Methods: DNA samples from 47 patients with AIPC enrolled in a randomized phase II trial using docetaxel and thalidomide vs. docetaxel alone were genotyped using the DMET 1.0 panel. Patients’ response was determined using RECIST criteria. Toxicities were graded using the NCI-CTC, and patients were identified if they experienced grade 3 or 4 toxicity. Given the distinct side effect profiles of these two drugs, specific toxicities were assigned as being due to either docetaxel or thalidomide. An association between the SNP parameters and clinical response or toxicity was tested using Mehta’s modification to Fisher’s exact test. Reported results were limited to those where p No significant financial relationships to disclose.

13078 Background: Pharmacogenetic testing of UGT1A1*28, a promoter variant of UGT1A1 gene, for estimating a risk of irinotecan toxicity has been introduced into clinical practice. Purpose: To elucidate clinical significance of UGT1A1*6 and UGT1A1*27, the variants in exon 1 that are found mostly in Asians. Methods: Pharmacogenetic relationships were explored between the genotyping results and ratio of area under the concentration-time curve (AUC) of SN-38 and its glucuronide (SN-38G) as a surrogate for a UGT1A1 activity (AUCSN-38/AUCSN-38G) in 36 Japanese patients who received various regimens of irinotecan chemotherapy at doses from 50 to 180 mg/m2. Results: No patients were homozygous for UGT1A1*28 and none had UGT1A1*27. One was heterozygous for UGT1A1*28. Two were homozygous and ten heterozygous for UGT1A1*6, all of whom were wild type with respect to UGT1A1*28. Two patients were simultaneously heterozygous for UGT1A1*28 and UGT1A1*6 that existed on the different chromosomes. The remaining 21 patients did not have any variants studied. The 2 patients who was simultaneously heterozygous for UGT1A1*28 and UGT1A1*6 and the 2 patients who were homozygous for UGT1A1*6 had significantly higher AUCSN-38/AUCSN-38G than the others (P = 0.004). Conclusions: Concurrence of the two UGT1A1 variants, UGT1A1*28 and UGT1A1*6 even in their heterozygous statuses, remarkably altered drug disposition of irinotecan and could enhance susceptibility to the drug. Patients who are homozygous for UGT1A1*6 should also be monitored cautiously. Genotyping of UGT1A1 polymorphisms in the coding region together with UGT1A1*28 is necessary for predicting irinotecan toxicity at least for Asian patient population. [Table: see text] [Table: see text]

13018 Background: Retrospective studies suggest TS polymorphisms predict toxicity from TS inhibitors as well as therapeutic response. The TS promoter has a variable number of tandem repeats (VNTR) polymorphism containing putative E-box binding sites that bind upstream stimulatory factor (USF) -1 and -2. One E-box binding site exists in TSER*2 and 2 binding sites exist in TSER*3. A single nucleotide polymorphism (SNP) at position 12 (G→C) in TSER*3’s 2nd repeat abolishes binding of USF-1/2. Combined effects of VNTR and SNP means individuals may have 2, 3 or 4 enhancer regions. We hypothesized that decreased enhancer numbers predicts for patients at risk for grade ≥3 mucositis, diarrhea, neutropenia, and overall toxicity and performed a prospective pharmacogenetic study of TS polymorphisms in adjuvant colon cancer patients treated with 5-FU/LV. Methods: High risk Stage II or Stage III colon cancer patients treated with 5FU/LV (425 mg/m2/ 20 mg/m2) daily for 5 days every 4 weeks had blood drawn for genotyping prior to starting therapy. Patients were assessed for toxicity using NCI CTC 2.0 in cycle 1. Three year disease-free survival will also be assessed. Results: 103 patients were enrolled and genotyped with 95 evaluable for toxicity. Patient characteristics: median age 61yrs (36–79): M 52%/F 48%; Stage III 77%, Stage II 23%. Frequency of genotypes containing 2 enhancers (TSER*2/ TSER*2, TSER*2 / TSER*3C, TSER*3C/ TSER*3C), 3 enhancers (TSER*2/ TSER*3G, TSER*3C/ TSER*3G) and 4 enhancers (TSER*3G/ TSER*3G) was 0.64, 0.31, and 0.05 respectively. No significant difference was seen in overall toxicity, mucositis, diarrhea and neutropenia based on TS polymorphism genotypes. Frequency of recurrence in 2 enhancer patients was 13% versus 26% in 3/4 enhancer patients but this did not reach statistical significance (p = 0.16). Conclusions: This prospective study does not confirm previously published retrospective studies suggesting that TS VNTR and SNP predict toxicity from TS inhibitors in patients treated with 5-fluorouracil for colon cancer. There is a trend for prediction of recurrence which requires further follow-up. No significant financial relationships to disclose.

2005 Background: Different polymorphisms (P) of the enzymes involved in C metabolism could be responsible of the different efficacy and toxicity in patients treated with C. Carboxylesterase (CES) a...

2010 Background: CPT-11 is oxidized to inactivated metabolites (including APC) by CYP3A enzymes and activated to SN-38 by carboxylesterase-2 (CES-2). SN-38 is inactivated to it glucuronide (SN-38G) by UGT1A1 and UGT1A9. Other enzymes and ABC transporters are involved in pathways of CPT-11 disposition. We had previously measured the plasma PK of patients treated with CPT-11 and analyzed the correlation with UGT1A1 variants. This study aims to generate hypotheses regarding the phenotypic effects of variation in other drug metabolizing and transporter genes. Methods: CPT-11, SN-38, and SN-38G AUCs were measured after a 350 mg/m2 IV dose in 64 adults with refractory solid tumors as part of a pharmacogenetic study. Genotyping of common variants (q>0.10) was performed for the following genes (number of variants in parenthesis): CES-2 (n=2), ABCC1 (n=7), ABCC2 (n=6), and ABCB1 (n=8). CYP3A4*1B, CYP3A5*3, UGT1A9 -11810T/9T and HNF1 79A>C were also typed. Results: The synonymous 3972T>C variant in ABCC2 was correl...